UMAP
plot_grid(ncol = 2, DimPlot(alldata, reduction = "umap", group.by = "orig.ident", shuffle = TRUE) +
NoLegend() + NoAxes(),
DimPlot(alldata, reduction = "umap", group.by = "Type", label = TRUE, shuffle = TRUE) +
NoLegend() + NoAxes(),
DimPlot(alldata, reduction = "umap", group.by = "Treatment", shuffle = TRUE) +
theme(legend.position = "bottom") + NoAxes())
FeaturePlot(alldata, reduction = "umap", features = c("Ptprc","Epcam"),
order = T, slot = "data", combine = T)
FeaturePlot(alldata, reduction = "umap", features = c("Ptprc"),
order = T, slot = "data", combine = T, split.by = "Type")
FeaturePlot(alldata, reduction = "umap", features = c("Epcam"),
order = T, slot = "data", combine = T, split.by = "Type")
sessionInfo()
## R version 4.0.5 (2021-03-31)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: macOS Catalina 10.15.7
##
## Matrix products: default
## BLAS/LAPACK: /Users/jenfra/miniconda3/envs/singlecell/lib/libopenblasp-r0.3.15.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ggplot2_3.3.6 cowplot_1.1.1 sp_1.5-0 SeuratObject_4.1.0
## [5] Seurat_4.1.1
##
## loaded via a namespace (and not attached):
## [1] Rtsne_0.15 colorspace_2.0-3 deldir_1.0-6
## [4] ellipsis_0.3.2 ggridges_0.5.3 rstudioapi_0.13
## [7] spatstat.data_2.2-0 farver_2.1.0 leiden_0.3.9
## [10] listenv_0.8.0 ggrepel_0.9.1 fansi_1.0.3
## [13] codetools_0.2-18 splines_4.0.5 cachem_1.0.6
## [16] knitr_1.37 polyclip_1.10-0 jsonlite_1.8.0
## [19] ica_1.0-2 cluster_2.1.2 png_0.1-7
## [22] rgeos_0.5-9 uwot_0.1.11 shiny_1.7.2
## [25] sctransform_0.3.3 spatstat.sparse_2.1-1 compiler_4.0.5
## [28] httr_1.4.2 assertthat_0.2.1 Matrix_1.4-1
## [31] fastmap_1.1.0 lazyeval_0.2.2 cli_3.3.0
## [34] later_1.3.0 htmltools_0.5.3 tools_4.0.5
## [37] igraph_1.3.4 gtable_0.3.0 glue_1.6.2
## [40] RANN_2.6.1 reshape2_1.4.4 dplyr_1.0.9
## [43] Rcpp_1.0.9 scattermore_0.8 jquerylib_0.1.4
## [46] vctrs_0.4.1 nlme_3.1-155 progressr_0.10.0
## [49] lmtest_0.9-40 spatstat.random_2.2-0 xfun_0.31
## [52] stringr_1.4.0 globals_0.16.0 mime_0.12
## [55] miniUI_0.1.1.1 lifecycle_1.0.1 irlba_2.3.5
## [58] goftest_1.2-3 future_1.27.0 MASS_7.3-55
## [61] zoo_1.8-9 scales_1.1.1 spatstat.core_2.4-4
## [64] promises_1.2.0.1 spatstat.utils_2.3-1 parallel_4.0.5
## [67] RColorBrewer_1.1-2 yaml_2.3.5 reticulate_1.25
## [70] pbapply_1.5-0 gridExtra_2.3 sass_0.4.0
## [73] rpart_4.1.16 stringi_1.7.8 highr_0.9
## [76] rlang_1.0.4 pkgconfig_2.0.3 matrixStats_0.62.0
## [79] evaluate_0.15 lattice_0.20-45 tensor_1.5
## [82] ROCR_1.0-11 purrr_0.3.4 labeling_0.4.2
## [85] patchwork_1.1.1 htmlwidgets_1.5.4 tidyselect_1.1.2
## [88] parallelly_1.32.1 RcppAnnoy_0.0.19 plyr_1.8.7
## [91] magrittr_2.0.3 bookdown_0.24 R6_2.5.1
## [94] generics_0.1.3 DBI_1.1.3 withr_2.5.0
## [97] mgcv_1.8-39 pillar_1.8.0 fitdistrplus_1.1-8
## [100] survival_3.3-1 abind_1.4-5 tibble_3.1.8
## [103] future.apply_1.8.1 KernSmooth_2.23-20 utf8_1.2.2
## [106] spatstat.geom_2.4-0 plotly_4.10.0 rmarkdown_2.13
## [109] grid_4.0.5 data.table_1.14.2 digest_0.6.29
## [112] xtable_1.8-4 tidyr_1.2.0 httpuv_1.6.5
## [115] munsell_0.5.0 viridisLite_0.4.0 bslib_0.4.0
